6z2d: Difference between revisions

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<StructureSection load='6z2d' size='340' side='right'caption='[[6z2d]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='6z2d' size='340' side='right'caption='[[6z2d]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6z2d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Akkm8 Akkm8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z2D FirstGlance]. <br>
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z2D FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.899&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Amuc_1119 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=349741 AKKM8])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6z2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z2d OCA], [https://pdbe.org/6z2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z2d RCSB], [https://www.ebi.ac.uk/pdbsum/6z2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z2d ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6z2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z2d OCA], [https://pdbe.org/6z2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z2d RCSB], [https://www.ebi.ac.uk/pdbsum/6z2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z2d ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Akkermansia muciniphila is a mucin-degrading bacterium commonly found in the human gut that promotes a beneficial effect on health, likely based on the regulation of mucus thickness and gut barrier integrity, but also on the modulation of the immune system. In this work, we focus in OgpA from A. muciniphila, an O-glycopeptidase that exclusively hydrolyzes the peptide bond N-terminal to serine or threonine residues substituted with an O-glycan. We determine the high-resolution X-ray crystal structures of the unliganded form of OgpA, the complex with the glycodrosocin O-glycopeptide substrate and its product, providing a comprehensive set of snapshots of the enzyme along the catalytic cycle. In combination with O-glycopeptide chemistry, enzyme kinetics, and computational methods we unveil the molecular mechanism of O-glycan recognition and specificity for OgpA. The data also contribute to understanding how A. muciniphila processes mucins in the gut, as well as analysis of post-translational O-glycosylation events in proteins.
Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila.,Trastoy B, Naegeli A, Anso I, Sjogren J, Guerin ME Nat Commun. 2020 Sep 24;11(1):4844. doi: 10.1038/s41467-020-18696-y. PMID:32973204<ref>PMID:32973204</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6z2d" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Akkm8]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Anso, I]]
[[Category: Anso I]]
[[Category: Guerin, M E]]
[[Category: Guerin ME]]
[[Category: Naegali, A]]
[[Category: Naegali A]]
[[Category: Sjogren, J]]
[[Category: Sjogren J]]
[[Category: Trastoy, B]]
[[Category: Trastoy B]]
[[Category: Hydrolase]]
[[Category: Mucin]]
[[Category: O-glycan endopeptidase]]
[[Category: Ogpa. metalloprotease]]
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